MacDNAsis Analysis

 Figure 1.  MacDNAsis analysis to determine the largest orf (open reading frame) of Mus musculus DNA helicase protein.  In the figure, red triangles indicate start codons and green lines indicate stop codons; the large black area with the arrow pointing to it is the largest orf and consists of 2283 bp.  To see the original Mus musculus DNA helicase cDNA, click here.

Figure 2.  The translation of DNA helicase cDNA to protein.  From the figure one can determine the percent compostion of DNA helicase by amino acid, and its molecular weight in daltons, which is 86823.50 daltons.

Figure 3.  A hydropathy plot of DNA helicase using the Kyte and Doolittle method.  Though DNA helicase is not an integral membrane protein, the hydropathy plot suggests that it is, as it contains many regions that exceed the 2.00 limit.  This discrepancy is most likely due to the small size of the graphing window.  If the window were increased one would most likely find that the plot contains no regions that exceed the 2.00 limit, thus properly classifying DNA helicase as a non-integral membrane protein.

Figure 4.     Antigenicity plot of Mus musculus DNA helicase.  The best region to use as a receptor for an antibody would be the most hydrophilic regions of the protein, corresponding to amino acid residues 275-285 and 685-692.

Figure 6. Representation of the secondary structure of mouse DNA helicase.  To compare this to the rasmol quarternary structure of DNA helicase in Bacillus stearothermophilus, click here
Figure 7.  A sample of the results of a multiple sequence alignment of DNA helicase found in humans, mice, yeast, malarial parasite, and bacteria.  In the figure, Untitled 6 is from bacteria, 5 is from malarial parastie, 4 is from yeast, 3 is from human, and 1 is from mouse.  The black boxes indicate shared amino acids, and, as you can tell from the alignment, there isn't much similiarity between the amino acid sequences of DNA helicase in these different organisms.

Figure 8.    Phylogentic tree of DNA helicase constructed using degree of amino acid conservation over time. As you can tell, there is not a high degree of amino acid conservation over time in DNA helicase in these five organisms, where untitled 6 is bacteria, 5 is malarial parasite, 4 is yeast, 3 is human, and 1 is mouse.  The highest degree of conservation is 11.1 % between malarial parasite and human DNA helicase.  The overall conservation is 4.8 %.

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